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Anaerobic degradation of syringic acid by an adapted strain of Rhodopseudomonas palustris.

Oshlag JZ, Ma Y, Morse K, Burger BT, Lemke RA, Karlen SD, Myers KS, Donohue TJ, Noguera DR.

Appl Environ Microbiol. 2019 Nov 15. pii: AEM.01888-19. doi: 10.1128/AEM.01888-19. [Epub ahead of print]


Medium-chain fatty acid synthesis by Candidatus Weimeria bifida, gen. nov., sp. nov., and Candidatus Pseudoramibacter fermentans, sp. nov.

Scarborough MJ, Myers KS, Donohue TJ, Noguera DR.

Appl Environ Microbiol. 2019 Nov 8. pii: AEM.02242-19. doi: 10.1128/AEM.02242-19. [Epub ahead of print]


Discovery of the extracytoplasmic function σ factors.

Lonetto MA, Donohue TJ, Gross CA, Buttner MJ.

Mol Microbiol. 2019 Aug;112(2):348-355. doi: 10.1111/mmi.14307. Epub 2019 Jun 17. Review.


Shedding light on a Group IV (ECF11) alternative σ factor.

Donohue TJ.

Mol Microbiol. 2019 Aug;112(2):374-384. doi: 10.1111/mmi.14280. Epub 2019 May 31. Review.


A heterodimeric glutathione S-transferase that stereospecifically breaks lignin's β(R)-aryl ether bond reveals the diversity of bacterial β-etherases.

Kontur WS, Olmsted CN, Yusko LM, Niles AV, Walters KA, Beebe ET, Vander Meulen KA, Karlen SD, Gall DL, Noguera DR, Donohue TJ.

J Biol Chem. 2019 Feb 8;294(6):1877-1890. doi: 10.1074/jbc.RA118.006548. Epub 2018 Dec 12.


Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome.

Scarborough MJ, Lawson CE, Hamilton JJ, Donohue TJ, Noguera DR.

mSystems. 2018 Nov 20;3(6). pii: e00221-18. doi: 10.1128/mSystems.00221-18. eCollection 2018 Nov-Dec.


Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production.

Scarborough MJ, Lynch G, Dickson M, McGee M, Donohue TJ, Noguera DR.

Biotechnol Biofuels. 2018 Jul 19;11:200. doi: 10.1186/s13068-018-1193-x. eCollection 2018.


Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin.

Kontur WS, Bingman CA, Olmsted CN, Wassarman DR, Ulbrich A, Gall DL, Smith RW, Yusko LM, Fox BG, Noguera DR, Coon JJ, Donohue TJ.

J Biol Chem. 2018 Apr 6;293(14):4955-4968. doi: 10.1074/jbc.RA117.001268. Epub 2018 Feb 15.


In Vitro Enzymatic Depolymerization of Lignin with Release of Syringyl, Guaiacyl, and Tricin Units.

Gall DL, Kontur WS, Lan W, Kim H, Li Y, Ralph J, Donohue TJ, Noguera DR.

Appl Environ Microbiol. 2018 Jan 17;84(3). pii: e02076-17. doi: 10.1128/AEM.02076-17. Print 2018 Feb 1.


Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides.

Burger BT, Imam S, Scarborough MJ, Noguera DR, Donohue TJ.

mSystems. 2017 Jun 6;2(3). pii: e00015-17. doi: 10.1128/mSystems.00015-17. eCollection 2017 May-Jun.


Mutations That Alter the Bacterial Cell Envelope Increase Lipid Production.

Lemmer KC, Zhang W, Langer SJ, Dohnalkova AC, Hu D, Lemke RA, Piotrowski JS, Orr G, Noguera DR, Donohue TJ.

MBio. 2017 May 23;8(3). pii: e00513-17. doi: 10.1128/mBio.00513-17.


Biochemical transformation of lignin for deriving valued commodities from lignocellulose.

Gall DL, Ralph J, Donohue TJ, Noguera DR.

Curr Opin Biotechnol. 2017 Jun;45:120-126. doi: 10.1016/j.copbio.2017.02.015. Epub 2017 Mar 24. Review.


Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges.

Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL.

MBio. 2016 May 13;7(3). pii: e00714-16. doi: 10.1128/mBio.00714-16.


Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.

Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD.

J Biol Chem. 2016 May 6;291(19):10228-38. doi: 10.1074/jbc.M115.700427. Epub 2016 Mar 3.


Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes.

Spero MA, Brickner JR, Mollet JT, Pisithkul T, Amador-Noguez D, Donohue TJ.

J Bacteriol. 2016 Mar 31;198(8):1268-80. doi: 10.1128/JB.01025-15. Print 2016 Apr.


Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin.

Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN Jr.

J Biol Chem. 2016 Mar 4;291(10):5234-46. doi: 10.1074/jbc.M115.694307. Epub 2015 Dec 4.


MICROBIOME. A unified initiative to harness Earth's microbiomes.

Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA; Unified Microbiome Initiative Consortium.

Science. 2015 Oct 30;350(6260):507-8. doi: 10.1126/science.aac8480. Epub 2015 Oct 28. No abstract available.


A Cardiolipin-Deficient Mutant of Rhodobacter sphaeroides Has an Altered Cell Shape and Is Impaired in Biofilm Formation.

Lin TY, Santos TM, Kontur WS, Donohue TJ, Weibel DB.

J Bacteriol. 2015 Nov;197(21):3446-55. doi: 10.1128/JB.00420-15. Epub 2015 Aug 17.


Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris.

Austin S, Kontur WS, Ulbrich A, Oshlag JZ, Zhang W, Higbee A, Zhang Y, Coon JJ, Hodge DB, Donohue TJ, Noguera DR.

Environ Sci Technol. 2015 Jul 21;49(14):8914-22. doi: 10.1021/acs.est.5b02062. Epub 2015 Jul 9.


Phylogenomic analysis and predicted physiological role of the proton-translocating NADH:quinone oxidoreductase (complex I) across bacteria.

Spero MA, Aylward FO, Currie CR, Donohue TJ.

MBio. 2015 Apr 14;6(2). pii: e00389-15. doi: 10.1128/mBio.00389-15.


Oxygen-dependent regulation of bacterial lipid production.

Lemmer KC, Dohnalkova AC, Noguera DR, Donohue TJ.

J Bacteriol. 2015 May;197(9):1649-58. doi: 10.1128/JB.02510-14. Epub 2015 Mar 2.


An integrated approach to reconstructing genome-scale transcriptional regulatory networks.

Imam S, Noguera DR, Donohue TJ.

PLoS Comput Biol. 2015 Feb 27;11(2):e1004103. doi: 10.1371/journal.pcbi.1004103. eCollection 2015 Feb.


CceR and AkgR regulate central carbon and energy metabolism in alphaproteobacteria.

Imam S, Noguera DR, Donohue TJ.

MBio. 2015 Feb 3;6(1). pii: e02461-14. doi: 10.1128/mBio.02461-14.


Global analysis of photosynthesis transcriptional regulatory networks.

Imam S, Noguera DR, Donohue TJ.

PLoS Genet. 2014 Dec 11;10(12):e1004837. doi: 10.1371/journal.pgen.1004837. eCollection 2014 Dec.


Quantifying the effects of light intensity on bioproduction and maintenance energy during photosynthetic growth of Rhodobacter sphaeroides.

Imam S, Fitzgerald CM, Cook EM, Donohue TJ, Noguera DR.

Photosynth Res. 2015 Feb;123(2):167-82. doi: 10.1007/s11120-014-0061-1. Epub 2014 Nov 27.


A group of sequence-related sphingomonad enzymes catalyzes cleavage of β-aryl ether linkages in lignin β-guaiacyl and β-syringyl ether dimers.

Gall DL, Ralph J, Donohue TJ, Noguera DR.

Environ Sci Technol. 2014 Oct 21;48(20):12454-63. doi: 10.1021/es503886d. Epub 2014 Oct 1.


Development of a GC/Quadrupole-Orbitrap mass spectrometer, part I: design and characterization.

Peterson AC, Hauschild JP, Quarmby ST, Krumwiede D, Lange O, Lemke RA, Grosse-Coosmann F, Horning S, Donohue TJ, Westphall MS, Coon JJ, Griep-Raming J.

Anal Chem. 2014 Oct 21;86(20):10036-43. doi: 10.1021/ac5014767. Epub 2014 Sep 10.


Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, Ma J, Markowitz V, Moore ER, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP.

PLoS Biol. 2014 Aug 5;12(8):e1001920. doi: 10.1371/journal.pbio.1001920. eCollection 2014 Aug.


Synthesis and scavenging role of furan fatty acids.

Lemke RA, Peterson AC, Ziegelhoffer EC, Westphall MS, Tjellström H, Coon JJ, Donohue TJ.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3450-7. doi: 10.1073/pnas.1405520111. Epub 2014 Aug 4.


A Rhodobacter sphaeroides protein mechanistically similar to Escherichia coli DksA regulates photosynthetic growth.

Lennon CW, Lemmer KC, Irons JL, Sellman MI, Donohue TJ, Gourse RL, Ross W.

MBio. 2014 Apr 29;5(3):e01105-14. doi: 10.1128/mBio.01105-14.


Prospective chest pain evaluation in the emergency department with use of high-sensitivity C-reactive protein (PROCEED-CRP study).

Ionescu CN, Chrissoheris MP, Slim HB, Slade M, Oen-Hsiao J, Donohue TJ, Bekui A, Ghantous AE.

Conn Med. 2014 Mar;78(3):133-8.


Stereochemical features of glutathione-dependent enzymes in the Sphingobium sp. strain SYK-6 β-aryl etherase pathway.

Gall DL, Kim H, Lu F, Donohue TJ, Noguera DR, Ralph J.

J Biol Chem. 2014 Mar 21;289(12):8656-67. doi: 10.1074/jbc.M113.536250. Epub 2014 Feb 7.


Global insights into energetic and metabolic networks in Rhodobacter sphaeroides.

Imam S, Noguera DR, Donohue TJ.

BMC Syst Biol. 2013 Sep 13;7:89. doi: 10.1186/1752-0509-7-89.


Psychosocial and cardiac outcomes of yoga for ICD patients: a randomized clinical control trial.

Toise SC, Sears SF, Schoenfeld MH, Blitzer ML, Marieb MA, Drury JH, Slade MD, Donohue TJ.

Pacing Clin Electrophysiol. 2014 Jan;37(1):48-62. doi: 10.1111/pace.12252. Epub 2013 Aug 26.


Benzoyl coenzyme a pathway-mediated metabolism of meta-hydroxy-aromatic acids in Rhodopseudomonas palustris.

Gall DL, Ralph J, Donohue TJ, Noguera DR.

J Bacteriol. 2013 Sep;195(18):4112-20. doi: 10.1128/JB.00634-13. Epub 2013 Jul 12.


Chemistry and combustion of fit-for-purpose biofuels.

Rothamer DA, Donohue TJ.

Curr Opin Chem Biol. 2013 Jun;17(3):522-8. doi: 10.1016/j.cbpa.2013.03.039. Epub 2013 May 8. Review.


Proteins needed to activate a transcriptional response to the reactive oxygen species singlet oxygen.

Nam TW, Ziegelhoffer EC, Lemke RA, Donohue TJ.

MBio. 2013 Jan 8;4(1):e00541-12. doi: 10.1128/mBio.00541-12.


Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome.

Kontur WS, Schackwitz WS, Ivanova N, Martin J, Labutti K, Deshpande S, Tice HN, Pennacchio C, Sodergren E, Weinstock GM, Noguera DR, Donohue TJ.

J Bacteriol. 2012 Dec;194(24):7016-7. doi: 10.1128/JB.01214-12.


Signal correlations in ecological niches can shape the organization and evolution of bacterial gene regulatory networks.

Dufour YS, Donohue TJ.

Adv Microb Physiol. 2012;61:1-36. doi: 10.1016/B978-0-12-394423-8.00001-9. Review.


Convergence of the transcriptional responses to heat shock and singlet oxygen stresses.

Dufour YS, Imam S, Koo BM, Green HA, Donohue TJ.

PLoS Genet. 2012 Sep;8(9):e1002929. doi: 10.1371/journal.pgen.1002929. Epub 2012 Sep 13.


Extracytoplasmic function σ factors of the widely distributed group ECF41 contain a fused regulatory domain.

Wecke T, Halang P, Staroń A, Dufour YS, Donohue TJ, Mascher T.

Microbiologyopen. 2012 Jun;1(2):194-213. doi: 10.1002/mbo3.22.


Nanolitre-scale crystallization using acoustic liquid-transfer technology.

Villaseñor AG, Wong A, Shao A, Garg A, Donohue TJ, Kuglstatter A, Harris SF.

Acta Crystallogr D Biol Crystallogr. 2012 Aug;68(Pt 8):893-900. doi: 10.1107/S0907444912016617. Epub 2012 Jul 17.


Conservation of thiol-oxidative stress responses regulated by SigR orthologues in actinomycetes.

Kim MS, Dufour YS, Yoo JS, Cho YB, Park JH, Nam GB, Kim HM, Lee KL, Donohue TJ, Roe JH.

Mol Microbiol. 2012 Jul;85(2):326-44. doi: 10.1111/j.1365-2958.2012.08115.x. Epub 2012 Jun 14.


Natural history of the Sprint Fidelis lead: survival analysis from a large single-center study.

Tzogias L, Bellavia D, Sharma S, Donohue TJ, Schoenfeld MH.

J Interv Card Electrophysiol. 2012 Jun;34(1):37-44. doi: 10.1007/s10840-011-9647-0.


Maximizing reductant flow into microbial H2 production.

Kontur WS, Noguera DR, Donohue TJ.

Curr Opin Biotechnol. 2012 Jun;23(3):382-9. doi: 10.1016/j.copbio.2011.10.003. Epub 2011 Oct 28. Review.


Pathways involved in reductant distribution during photobiological H(2) production by Rhodobacter sphaeroides.

Kontur WS, Ziegelhoffer EC, Spero MA, Imam S, Noguera DR, Donohue TJ.

Appl Environ Microbiol. 2011 Oct;77(20):7425-9. doi: 10.1128/AEM.05273-11. Epub 2011 Aug 19.


iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network.

Imam S, Yilmaz S, Sohmen U, Gorzalski AS, Reed JL, Noguera DR, Donohue TJ.

BMC Syst Biol. 2011 Jul 21;5:116. doi: 10.1186/1752-0509-5-116.


Features of Rhodobacter sphaeroides ChrR required for stimuli to promote the dissociation of σ(E)/ChrR complexes.

Greenwell R, Nam TW, Donohue TJ.

J Mol Biol. 2011 Apr 8;407(4):477-91. doi: 10.1016/j.jmb.2011.01.055. Epub 2011 Feb 3.


An insect herbivore microbiome with high plant biomass-degrading capacity.

Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA, Bouffard P, Li L, Osterberger J, Harkins TT, Slater SC, Donohue TJ, Currie CR.

PLoS Genet. 2010 Sep 23;6(9):e1001129. doi: 10.1371/journal.pgen.1001129.


Reconstruction of the core and extended regulons of global transcription factors.

Dufour YS, Kiley PJ, Donohue TJ.

PLoS Genet. 2010 Jul 22;6(7):e1001027. doi: 10.1371/journal.pgen.1001027.

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